Although many tests have been developed to diagnose infection, many of these tests are only specific and/or sensitive when there is a high load of the infectious agent present, i.e. in the case of late or advanced stages of infection. In addition, some of these tests require highly technical personnel or specialized knowledge to carry out the tests.
For example, to date, there is no robust test available for detecting high risk strains of HPV in pap smears, and which is both clinically sensitive and specific, as well as convenient, easy and inexpensive, without the need for highly trained personnel. (Kurtycz et al., Comparison of Methods Trial for High-Risk HPV Diagnostic Cytopathology 38:104-108 (2009); Ginocchio et al., Comparison of the Third Wave Invader Human Papilloma (HPV) Assay and the Digene HPV Hybrid Capture 2 Assay for Detection of High-Risk HPV DNA J. Clin. Microbiol. 46:1641-1646 (2008)). The Pap or Papanicolau test is currently the test of choice for the initial screening of pre-malignant or malignant cervical cancers caused by HPV. The Pap test is a cytology test which requires highly trained personnel to discriminate between normal cells and cells undergoing malignant lesions under a light microscope. The Diagene-HC2 DNA test, which is the only FDA-market approved HPV test, relies on the capture of DNA/RNA hybrids on a solid phase. The captured DNA/RNA hybrids are detected using an enzyme-linked antibody upon amplification. Although the test can detect up to thirteen HPV types, it has poor sensitivity (5000 copies/mL) and specificity. Furthermore, the test requires purification of DNA from the sample and it cross-hybridizes with low-risk and high-risk HPV types when the viral load in the sample is high.
Other tests for HPV include GenProbe's Aptima HPV test, Third Wave's Invader HPV DNA test, Ventana's Inform1 HPV in-situ hybridization test, and other PCR-based tests, including Roche's Amplicor or Linear Array HPV DNA tests. These tests require purification of the nucleic acid from the samples and/or amplification of the target nucleic acids prior to detection, which can result in poor sensitivity or specificity. In addition, these tests can be expensive and time-consuming. Furthermore, since most of these tests require amplification of the target polynucleotides, a highly clean and dedicated environment is required to ensure that there is no carry over or cross contamination between samples.
Accordingly, there is a need for an efficient, rapid, reliable, and inexpensive method and/or assay for detecting an infectious agent, such as HPV, and which has the desired level of sensitivity and specificity for screening and/or evaluating samples for the presence or level of the infectious agent.